Well, to be clear, when I updated my Nexus 7 (2013) from 4.4.4 to 5.0.1, it automatically migrated ALL of my email accounts to Gmail (a pop account, a hotmail account, and a work Exchange account, none of which had been in the Gmail account before the update). There was no "option" about it. I'm not sure there is any way to get them out of Gmail, other than completely deleting those accounts and then adding them back into some other email app. If there is, Gmail doesn't make it easy to find it. I downgraded back to 4.4.4, in large part because it ticked me off that Gmail hijacked all of my email accounts in this fashion.
The same thing happened when I authorized the Gmail app update on my Note 4 phone (running 4.4.4). Gmail updated and hijacked all of my email accounts into the Gmail app. I was able to uninstall the updates, and now I simply reject any requests to authorize updates to Gmail.